202 results on '"de la Iglesia, P."'
Search Results
2. Deep Learning for Precision Agriculture: Post-Spraying Evaluation and Deposition Estimation
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Rogers, Harry, Zebin, Tahmina, Cielniak, Grzegorz, De La Iglesia, Beatriz, and Magri, Ben
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Precision spraying evaluation requires automation primarily in post-spraying imagery. In this paper we propose an eXplainable Artificial Intelligence (XAI) computer vision pipeline to evaluate a precision spraying system post-spraying without the need for traditional agricultural methods. The developed system can semantically segment potential targets such as lettuce, chickweed, and meadowgrass and correctly identify if targets have been sprayed. Furthermore, this pipeline evaluates using a domain-specific Weakly Supervised Deposition Estimation task, allowing for class-specific quantification of spray deposit weights in {\mu}L. Estimation of coverage rates of spray deposition in a class-wise manner allows for further understanding of effectiveness of precision spraying systems. Our study evaluates different Class Activation Mapping techniques, namely AblationCAM and ScoreCAM, to determine which is more effective and interpretable for these tasks. In the pipeline, inference-only feature fusion is used to allow for further interpretability and to enable the automation of precision spraying evaluation post-spray. Our findings indicate that a Fully Convolutional Network with an EfficientNet-B0 backbone and inference-only feature fusion achieves an average absolute difference in deposition values of 156.8 {\mu}L across three classes in our test set. The dataset curated in this paper is publicly available at https://github.com/Harry-Rogers/PSIE
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- 2024
3. Medical mT5: An Open-Source Multilingual Text-to-Text LLM for The Medical Domain
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García-Ferrero, Iker, Agerri, Rodrigo, Salazar, Aitziber Atutxa, Cabrio, Elena, de la Iglesia, Iker, Lavelli, Alberto, Magnini, Bernardo, Molinet, Benjamin, Ramirez-Romero, Johana, Rigau, German, Villa-Gonzalez, Jose Maria, Villata, Serena, and Zaninello, Andrea
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Computer Science - Computation and Language ,Computer Science - Artificial Intelligence ,Computer Science - Machine Learning - Abstract
Research on language technology for the development of medical applications is currently a hot topic in Natural Language Understanding and Generation. Thus, a number of large language models (LLMs) have recently been adapted to the medical domain, so that they can be used as a tool for mediating in human-AI interaction. While these LLMs display competitive performance on automated medical texts benchmarks, they have been pre-trained and evaluated with a focus on a single language (English mostly). This is particularly true of text-to-text models, which typically require large amounts of domain-specific pre-training data, often not easily accessible for many languages. In this paper, we address these shortcomings by compiling, to the best of our knowledge, the largest multilingual corpus for the medical domain in four languages, namely English, French, Italian and Spanish. This new corpus has been used to train Medical mT5, the first open-source text-to-text multilingual model for the medical domain. Additionally, we present two new evaluation benchmarks for all four languages with the aim of facilitating multilingual research in this domain. A comprehensive evaluation shows that Medical mT5 outperforms both encoders and similarly sized text-to-text models for the Spanish, French, and Italian benchmarks, while being competitive with current state-of-the-art LLMs in English., Comment: LREC-COLING 2024
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- 2024
4. Advancing precision agriculture: domain-specific augmentations and robustness testing for convolutional neural networks in precision spraying evaluation
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Rogers, Harry, De La Iglesia, Beatriz, Zebin, Tahmina, Cielniak, Grzegorz, and Magri, Ben
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- 2024
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5. One-dimensional Continuous-Time Quantum Markov Chains: qubit probabilities and measures
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De la Iglesia, Manuel D. and Lardizabal, Carlos F.
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Quantum Physics ,Mathematical Physics ,Mathematics - Classical Analysis and ODEs ,81S22, 42C05 - Abstract
Quantum Markov chains (QMCs) are positive maps on a trace-class space describing open quantum dynamics on graphs. Such objects have a statistical resemblance with classical random walks, while at the same time it allows for internal (quantum) degrees of freedom. In this work we study continuous-time QMCs on the integer line, half-line and finite segments, so that we are able to obtain exact probability calculations in terms of the associated matrix-valued orthogonal polynomials and measures. The methods employed here are applicable to a wide range of settings, but we will restrict to classes of examples for which the Lindblad generators are induced by a single positive map, and such that the Stieltjes transforms of the measures and their inverses can be calculated explicitly., Comment: 21 pages, 3 figures
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- 2024
6. Reinforcement Learning for Blind Stair Climbing with Legged and Wheeled-Legged Robots
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Chamorro, Simon, Klemm, Victor, Valls, Miguel de la Iglesia, Pal, Christopher, and Siegwart, Roland
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Computer Science - Robotics - Abstract
In recent years, legged and wheeled-legged robots have gained prominence for tasks in environments predominantly created for humans across various domains. One significant challenge faced by many of these robots is their limited capability to navigate stairs, which hampers their functionality in multi-story environments. This study proposes a method aimed at addressing this limitation, employing reinforcement learning to develop a versatile controller applicable to a wide range of robots. In contrast to the conventional velocity-based controllers, our approach builds upon a position-based formulation of the RL task, which we show to be vital for stair climbing. Furthermore, the methodology leverages an asymmetric actor-critic structure, enabling the utilization of privileged information from simulated environments during training while eliminating the reliance on exteroceptive sensors during real-world deployment. Another key feature of the proposed approach is the incorporation of a boolean observation within the controller, enabling the activation or deactivation of a stair-climbing mode. We present our results on different quadrupeds and bipedal robots in simulation and showcase how our method allows the balancing robot Ascento to climb 15cm stairs in the real world, a task that was previously impossible for this robot., Comment: Video: https://youtu.be/Ec6ar8BVJh4
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- 2024
7. DeepCERES: A Deep learning method for cerebellar lobule segmentation using ultra-high resolution multimodal MRI
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Morell-Ortega, Sergio, Ruiz-Perez, Marina, Gadea, Marien, Vivo-Hernando, Roberto, Rubio, Gregorio, Aparici, Fernando, de la Iglesia-Vaya, Maria, Catheline, Gwenaelle, Coupé, Pierrick, and Manjón, José V.
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Quantitative Biology - Neurons and Cognition - Abstract
This paper introduces a novel multimodal and high-resolution human brain cerebellum lobule segmentation method. Unlike current tools that operate at standard resolution ($1 \text{ mm}^{3}$) or using mono-modal data, the proposed method improves cerebellum lobule segmentation through the use of a multimodal and ultra-high resolution ($0.125 \text{ mm}^{3}$) training dataset. To develop the method, first, a database of semi-automatically labelled cerebellum lobules was created to train the proposed method with ultra-high resolution T1 and T2 MR images. Then, an ensemble of deep networks has been designed and developed, allowing the proposed method to excel in the complex cerebellum lobule segmentation task, improving precision while being memory efficient. Notably, our approach deviates from the traditional U-Net model by exploring alternative architectures. We have also integrated deep learning with classical machine learning methods incorporating a priori knowledge from multi-atlas segmentation, which improved precision and robustness. Finally, a new online pipeline, named DeepCERES, has been developed to make available the proposed method to the scientific community requiring as input only a single T1 MR image at standard resolution., Comment: 20 pages
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- 2024
8. MadQCI: a heterogeneous and scalable SDN QKD network deployed in production facilities
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Martin, V., Brito, J. P., Ortiz, L., Mendez, R. B., Buruaga, J. S., Vicente, R. J., Sebastián-Lombraña, A., Rincon, D., Perez, F., Sanchez, C., Peev, M., Brunner, H. H., Fung, F., Poppe, A., Fröwis, F., Shields, A. J., Woodward, R. I., Griesser, H., Roehrich, S., De La Iglesia, F., Abellan, C., Hentschel, M., Rivas-Moscoso, J. M., Pastor, A., Folgueira, J., and Lopez, D. R.
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Quantum Physics - Abstract
Current quantum key distribution (QKD) networks focus almost exclusively on transporting secret keys with the highest possible rate. Consequently, they are built as mostly fixed, ad hoc, logically, and physically isolated infrastructures designed to avoid any penalty to the quantum channel. This architecture is neither scalable nor cost-effective and future, real-world deployments will differ considerably. The structure of the MadQCI QKD network presented here is based on disaggregated components and modern paradigms especially designed for flexibility, upgradability, and facilitating the integration of QKD in the security and telecommunications-networks ecosystem. These underlying ideas have been tested by deploying many QKD systems from several manufacturers in a real-world, multi-tenant telecommunications network, installed in production facilities and sharing the infrastructure with commercial traffic. Different technologies have been used in different links to address the variety of situations and needs that arise in real networks, exploring a wide range of possibilities. Finally, a set of realistic use cases have been implemented to demonstrate the validity and performance of the network. The testing took place during a period close to three years, where most of the nodes were continuously active.
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- 2023
9. Can Foundation Models Watch, Talk and Guide You Step by Step to Make a Cake?
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Bao, Yuwei, Yu, Keunwoo Peter, Zhang, Yichi, Storks, Shane, Bar-Yossef, Itamar, De La Iglesia, Alexander, Su, Megan, Zheng, Xiao Lin, and Chai, Joyce
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Computer Science - Artificial Intelligence ,Computer Science - Human-Computer Interaction - Abstract
Despite tremendous advances in AI, it remains a significant challenge to develop interactive task guidance systems that can offer situated, personalized guidance and assist humans in various tasks. These systems need to have a sophisticated understanding of the user as well as the environment, and make timely accurate decisions on when and what to say. To address this issue, we created a new multimodal benchmark dataset, Watch, Talk and Guide (WTaG) based on natural interaction between a human user and a human instructor. We further proposed two tasks: User and Environment Understanding, and Instructor Decision Making. We leveraged several foundation models to study to what extent these models can be quickly adapted to perceptually enabled task guidance. Our quantitative, qualitative, and human evaluation results show that these models can demonstrate fair performances in some cases with no task-specific training, but a fast and reliable adaptation remains a significant challenge. Our benchmark and baselines will provide a stepping stone for future work on situated task guidance., Comment: Accepted to EMNLP 2023 Findings
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- 2023
10. The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)
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Poldrack, Russell A., Markiewicz, Christopher J., Appelhoff, Stefan, Ashar, Yoni K., Auer, Tibor, Baillet, Sylvain, Bansal, Shashank, Beltrachini, Leandro, Benar, Christian G., Bertazzoli, Giacomo, Bhogawar, Suyash, Blair, Ross W., Bortoletto, Marta, Boudreau, Mathieu, Brooks, Teon L., Calhoun, Vince D., Castelli, Filippo Maria, Clement, Patricia, Cohen, Alexander L, Cohen-Adad, Julien, D'Ambrosio, Sasha, de Hollander, Gilles, de la iglesia-Vayá, María, de la Vega, Alejandro, Delorme, Arnaud, Devinsky, Orrin, Draschkow, Dejan, Duff, Eugene Paul, DuPre, Elizabeth, Earl, Eric, Esteban, Oscar, Feingold, Franklin W., Flandin, Guillaume, galassi, anthony, Gallitto, Giuseppe, Ganz, Melanie, Gau, Rémi, Gholam, James, Ghosh, Satrajit S., Giacomel, Alessio, Gillman, Ashley G, Gleeson, Padraig, Gramfort, Alexandre, Guay, Samuel, Guidali, Giacomo, Halchenko, Yaroslav O., Handwerker, Daniel A., Hardcastle, Nell, Herholz, Peer, Hermes, Dora, Honey, Christopher J., Innis, Robert B., Ioanas, Horea-Ioan, Jahn, Andrew, Karakuzu, Agah, Keator, David B., Kiar, Gregory, Kincses, Balint, Laird, Angela R., Lau, Jonathan C., Lazari, Alberto, Legarreta, Jon Haitz, Li, Adam, Li, Xiangrui, Love, Bradley C., Lu, Hanzhang, Maumet, Camille, Mazzamuto, Giacomo, Meisler, Steven L., Mikkelsen, Mark, Mutsaerts, Henk, Nichols, Thomas E., Nikolaidis, Aki, Nilsonne, Gustav, Niso, Guiomar, Norgaard, Martin, Okell, Thomas W, Oostenveld, Robert, Ort, Eduard, Park, Patrick J., Pawlik, Mateusz, Pernet, Cyril R., Pestilli, Franco, Petr, Jan, Phillips, Christophe, Poline, Jean-Baptiste, Pollonini, Luca, Raamana, Pradeep Reddy, Ritter, Petra, Rizzo, Gaia, Robbins, Kay A., Rockhill, Alexander P., Rogers, Christine, Rokem, Ariel, Rorden, Chris, Routier, Alexandre, Saborit-Torres, Jose Manuel, Salo, Taylor, Schirner, Michael, Smith, Robert E., Spisak, Tamas, Sprenger, Julia, Swann, Nicole C., Szinte, Martin, Takerkart, Sylvain, Thirion, Bertrand, Thomas, Adam G., Torabian, Sajjad, Varoquaux, Gael, Voytek, Bradley, Welzel, Julius, Wilson, Martin, Yarkoni, Tal, and Gorgolewski, Krzysztof J.
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Quantitative Biology - Other Quantitative Biology - Abstract
The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.
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- 2023
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11. MadQCI: a heterogeneous and scalable SDN-QKD network deployed in production facilities
- Author
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V. Martin, J. P. Brito, L. Ortíz, R. B. Méndez, J. S. Buruaga, R. J. Vicente, A. Sebastián-Lombraña, D. Rincón, F. Pérez, C. Sánchez, M. Peev, H. H. Brunner, F. Fung, A. Poppe, F. Fröwis, A. J. Shields, R. I. Woodward, H. Griesser, S. Roehrich, F. de la Iglesia, C. Abellán, M. Hentschel, J. M. Rivas-Moscoso, A. Pastor-Perales, J. Folgueira, and D. López
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Physics ,QC1-999 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Abstract Current quantum key distribution (QKD) networks focus almost exclusively on transporting secret keys at the highest possible rate. Consequently, they are built as mostly fixed, ad hoc, logically, and physically isolated infrastructures designed to avoid any penalty to the quantum channel. This architecture is neither scalable nor cost-effective and future, real-world deployments will differ considerably. The structure of the MadQCI QKD network presented here is based on disaggregated components and modern paradigms especially designed for flexibility, upgradability, and facilitating the integration of QKD in the security and telecommunications-networks ecosystem. These underlying ideas have been tested by deploying many QKD systems from several manufacturers in a real-world, multi-tenant telecommunications network, installed in production facilities and sharing the infrastructure with commercial traffic. Different technologies have been used in different links to address the variety of situations and needs that arise in real networks, exploring a wide range of possibilities. Finally, a set of realistic use cases has been implemented to demonstrate the validity and performance of the network. The testing took place during a period close to three years, where most of the nodes were continuously active.
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- 2024
- Full Text
- View/download PDF
12. EriBERTa: A Bilingual Pre-Trained Language Model for Clinical Natural Language Processing
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de la Iglesia, Iker, Atutxa, Aitziber, Gojenola, Koldo, and Barrena, Ander
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Computer Science - Computation and Language - Abstract
The utilization of clinical reports for various secondary purposes, including health research and treatment monitoring, is crucial for enhancing patient care. Natural Language Processing (NLP) tools have emerged as valuable assets for extracting and processing relevant information from these reports. However, the availability of specialized language models for the clinical domain in Spanish has been limited. In this paper, we introduce EriBERTa, a bilingual domain-specific language model pre-trained on extensive medical and clinical corpora. We demonstrate that EriBERTa outperforms previous Spanish language models in the clinical domain, showcasing its superior capabilities in understanding medical texts and extracting meaningful information. Moreover, EriBERTa exhibits promising transfer learning abilities, allowing for knowledge transfer from one language to another. This aspect is particularly beneficial given the scarcity of Spanish clinical data.
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- 2023
13. An AI-Ready Multiplex Staining Dataset for Reproducible and Accurate Characterization of Tumor Immune Microenvironment
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Ghahremani, Parmida, Marino, Joseph, Hernandez-Prera, Juan, de la Iglesia, Janis V., Slebos, Robbert JC, Chung, Christine H., and Nadeem, Saad
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Quantitative Biology - Quantitative Methods - Abstract
We introduce a new AI-ready computational pathology dataset containing restained and co-registered digitized images from eight head-and-neck squamous cell carcinoma patients. Specifically, the same tumor sections were stained with the expensive multiplex immunofluorescence (mIF) assay first and then restained with cheaper multiplex immunohistochemistry (mIHC). This is a first public dataset that demonstrates the equivalence of these two staining methods which in turn allows several use cases; due to the equivalence, our cheaper mIHC staining protocol can offset the need for expensive mIF staining/scanning which requires highly-skilled lab technicians. As opposed to subjective and error-prone immune cell annotations from individual pathologists (disagreement > 50%) to drive SOTA deep learning approaches, this dataset provides objective immune and tumor cell annotations via mIF/mIHC restaining for more reproducible and accurate characterization of tumor immune microenvironment (e.g. for immunotherapy). We demonstrate the effectiveness of this dataset in three use cases: (1) IHC quantification of CD3/CD8 tumor-infiltrating lymphocytes via style transfer, (2) virtual translation of cheap mIHC stains to more expensive mIF stains, and (3) virtual tumor/immune cellular phenotyping on standard hematoxylin images. The dataset is available at \url{https://github.com/nadeemlab/DeepLIIF}., Comment: MICCAI'23 (Early Accept). First two authors contributed equally. Forward correspondence to last two authors
- Published
- 2023
14. MetaFun: unveiling sex-based differences in multiple transcriptomic studies through comprehensive functional meta-analysis
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Pablo Malmierca-Merlo, Rubén Sánchez-Garcia, Rubén Grillo-Risco, Irene Pérez-Díez, José F. Català-Senent, María de la Iglesia-Vayá, Marta R. Hidalgo, and Francisco Garcia-Garcia
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Systematic review ,Meta-analysis ,Web tool ,RNA-sequencing ,Functional profiling ,Sex-based differences ,Medicine ,Physiology ,QP1-981 - Abstract
Abstract Background While sex-based differences in various health scenarios have been thoroughly acknowledged in the literature, we lack sufficient tools and methods that allow for an in-depth analysis of sex as a variable in biomedical research. To fill this knowledge gap, we created MetaFun as an easy-to-use web-based tool to meta-analyze multiple transcriptomic datasets with a sex-based perspective to gain major statistical power and biological soundness. Description MetaFun is a complete suite that allows the analysis of transcriptomics data and the exploration of the results at all levels, performing single-dataset exploratory analysis, differential gene expression, gene set functional enrichment, and finally, combining results in a functional meta-analysis. Which biological processes, molecular functions or cellular components are altered in a common pattern in different transcriptomic studies when comparing male and female patients? This and other biological questions of interest can be answered with the use of MetaFun. This tool is available at https://bioinfo.cipf.es/metafun while additional help can be found at https://gitlab.com/ubb-cipf/metafunweb/-/wikis/Summary . Conclusions Overall, Metafun is the first open-access web-based tool to identify consensus biological functions across multiple transcriptomic datasets, helping to elucidate sex differences in numerous diseases. Its use will facilitate the generation of novel biological knowledge that can be used in the research and application of Personalized Medicine considering the sex of patients.
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- 2024
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15. The impact of sex on gene expression in the brain of schizophrenic patients: a systematic review and meta-analysis of transcriptomic studies
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Hector Carceller, Marta R. Hidalgo, María José Escartí, Juan Nacher, Maria de la Iglesia-Vayá, and Francisco García-García
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Systematic review ,Meta-analysis ,Schizophrenia ,RNA-sequencing ,Prefrontal cortex ,Hippocampus ,Medicine ,Physiology ,QP1-981 - Abstract
Abstract Background Schizophrenia is a severe neuropsychiatric disorder characterized by altered perception, mood, and behavior that profoundly impacts patients and society despite its relatively low prevalence. Sex-based differences have been described in schizophrenia epidemiology, symptomatology and outcomes. Different studies explored the impact of schizophrenia in the brain transcriptome, however we lack a consensus transcriptomic profile that considers sex and differentiates specific cerebral regions. Methods We performed a systematic review on bulk RNA-sequencing studies of post-mortem brain samples. Then, we fulfilled differential expression analysis on each study and summarized their results with regions-specific meta-analyses (prefrontal cortex and hippocampus) and a global all-studies meta-analysis. Finally, we used the consensus transcriptomic profiles to functionally characterize the impact of schizophrenia in males and females by protein-protein interaction networks, enriched biological processes and dysregulated transcription factors. Results We discovered the sex-based dysregulation of 265 genes in the prefrontal cortex, 1.414 genes in the hippocampus and 66 genes in the all-studies meta-analyses. The functional characterization of these gene sets unveiled increased processes related to immune response functions in the prefrontal cortex in male and the hippocampus in female schizophrenia patients and the overexpression of genes related to neurotransmission and synapses in the prefrontal cortex of female schizophrenia patients. Considering a meta-analysis of all brain regions available, we encountered the relative overexpression of genes related to synaptic plasticity and transmission in females and the overexpression of genes involved in organizing genetic information and protein folding in male schizophrenia patients. The protein-protein interaction networks and transcription factors activity analyses supported these sex-based profiles. Conclusions Our results report multiple sex-based transcriptomic alterations in specific brain regions of schizophrenia patients, which provides new insight into the role of sex in schizophrenia. Moreover, we unveil a partial overlapping of inflammatory processes in the prefrontal cortex of males and the hippocampus of females.
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- 2024
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16. LOCAL ANTIBACTERIAL TREATMENT IN PATIENTS WITH INFECTED PANCREATIC WALLED-OFF NECROSIS: A SYSTEMATIC REVIEW
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Nizar R. Kerbazh, Daniel de la Iglesia, Jose Larino-Noia, Julio Iglesias-Garcia, Serhii I. Panasenko, and Juan E. Dominguez-Munoz
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pancreatic necrosis ,step-up approach ,infection ,local antibiotic infusion ,necrosectomy ,Medicine - Abstract
Introduction. Systemic antibacterial treatment in patients with infected pancreatic necrosis often fails to resolve the infection due to impaired penetration in necrotic areas. The endoscopic step-up approach based on endoscopic transmural drainage followed, if necessary, by endoscopic necrosectomy has become the standard of care in patients who do not respond to systemic antibiotics. The additional local administration of antibiotics may increase their concentration in necrotic tissue. Aim. To evaluate the efficacy of local infusion of antibacterial agents to the site of infection in addition to systemic treatment after endoscopic drainage to resolve the infection and decrease the need for necrosectomy in patients with walled-off infected pancreatic necrosis. Materials and methods. Major databases were searched for clinical studies assessing the efficacy of local perfusion of antibiotics for the treatment of infected pancreatic necrosis. Results. Four studies were included, two cohort studies and two single-case reports. The majority of patients with infected pancreatic necrosis developed polymicrobial infection. More than one-third of patients additionally had fungal infection. Local irrigation of antibiotics in patients with infected pancreatic necrosis resulted in the eradication of bacteria and fungi, avoiding necrosectomy in almost half of cases. No local or systemic side effects were reported with this strategy. Conclusions. Evidence evaluating the efficacy of local antibiotics for the treatment of infected pancreatic necrosis is scarce. Simultaneous local and systemic administration of antibiotics after endoscopic drainage could reduce the need for necrosectomy. Randomized clinical trials are needed to evaluate the impact of adding local to systemic antibiotics in the prognosis of patients with infected pancreatic necrosis.
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- 2024
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17. The bilateral birth-death chain generated by the associated Jacobi polynomials
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de la Iglesia, Manuel D. and Juarez, Claudia
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Mathematics - Probability ,Mathematics - Classical Analysis and ODEs ,60J10, 33C45, 42C05 - Abstract
We give a probabilistic interpretation of the associated Jacobi polynomials, which can be constructed from the three-term recurrence relation for the classical Jacobi polynomials by shifting the integer index $n$ by a real number $t$. Under certain restrictions, this will give rise to a doubly infinite tridiagonal stochastic matrix which can be interpreted as the one-step transition probability matrix of a discrete-time bilateral birth-death chain with state space on $\mathbb{Z}$. We also study the unique UL and LU stochastic factorizations of the transition probability matrix, as well as the discrete Darboux transformations and corresponding spectral matrices. Finally, we use all these results to provide an urn model on the integers for the associated Jacobi polynomials., Comment: 23 pages, 9 figures
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- 2023
18. QBD processes associated with Jacobi-Koornwinder bivariate polynomials and urn models
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Fernández, Lidia and de la Iglesia, Manuel D.
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Mathematics - Classical Analysis and ODEs ,Mathematics - Probability - Abstract
We study a family of quasi-birth-and-death (QBD) processes associated with the so-called first family of Jacobi-Koornwinder bivariate polynomials. These polynomials are orthogonal on a bounded region typically known as the swallow tail. We will explicitly compute the coefficients of the three-term recurrence relations generated by these QBD polynomials and study the conditions under we can produce families of discrete-time QBD processes. Finally, we show an urn model associated with one special case of these QBD processes., Comment: 14 pages, 3 figures. arXiv admin note: text overlap with arXiv:2002.04536
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- 2022
19. An integrated approach to identifying sex-specific genes, transcription factors, and pathways relevant to Alzheimer's disease
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Adolfo López-Cerdán, Zoraida Andreu, Marta R. Hidalgo, Irene Soler-Sáez, María de la Iglesia-Vayá, Akiko Mikozami, Franca R. Guerini, and Francisco García-García
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Alzheimer's disease ,Cognitive function ,meta-analysis ,Sex-based difference impact disease ,Transcriptomics ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Background: Age represents a significant risk factor for the development of Alzheimer's disease (AD); however, recent research has documented an influencing role of sex in several features of AD. Understanding the impact of sex on specific molecular mechanisms associated with AD remains a critical challenge to creating tailored therapeutic interventions. Methods: The exploration of the sex-based differential impact on disease (SDID) in AD used a systematic review to first select transcriptomic studies of AD with data regarding sex in the period covering 2002 to 2021 with a focus on the primary brain regions affected by AD - the cortex (CT) and the hippocampus (HP). A differential expression analysis for each study and two tissue-specific meta-analyses were then performed. Focusing on the CT due to the presence of significant SDID-related alterations, a comprehensive functional characterization was conducted: protein-protein network interaction and over-representation analyses to explore biological processes and pathways and a VIPER analysis to estimate transcription factor activity. Results: We selected 8 CT and 5 HP studies from the Gene Expression Omnibus (GEO) repository for tissue-specific meta-analyses. We detected 389 significantly altered genes in the SDID comparison in the CT. Generally, female AD patients displayed more affected genes than males; we grouped said genes into six subsets according to their expression profile in female and male AD patients. Only subset I (repressed genes in female AD patients) displayed significant results during functional profiling. Female AD patients demonstrated more significant impairments in biological processes related to the regulation and organization of synapsis and pathways linked to neurotransmitters (glutamate and GABA) and protein folding, Aβ aggregation, and accumulation compared to male AD patients. These findings could partly explain why we observe more pronounced cognitive decline in female AD patients. Finally, we detected 23 transcription factors with different activation patterns according to sex, with some associated with AD for the first time. All results generated during this study are readily available through an open web resource Metafun-AD (https://bioinfo.cipf.es/metafun-ad/). Conclusion: Our meta-analyses indicate the existence of differences in AD-related mechanisms in female and male patients. These sex-based differences will represent the basis for new hypotheses and could significantly impact precision medicine and improve diagnosis and clinical outcomes in AD patients.
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- 2024
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20. Deep Reinforcement Learning techniques for dynamic task offloading in the 5G edge-cloud continuum
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Gorka Nieto, Idoia de la Iglesia, Unai Lopez-Novoa, and Cristina Perfecto
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Task offloading ,Performance evaluation ,Energy consumption ,Reinforcement Learning (RL) ,Quality-of-Experience (QoE) ,Multi-access Edge Computing (MEC) ,Computer engineering. Computer hardware ,TK7885-7895 ,Electronic computers. Computer science ,QA75.5-76.95 - Abstract
Abstract The integration of new Internet of Things (IoT) applications and services heavily relies on task offloading to external devices due to the constrained computing and battery resources of IoT devices. Up to now, Cloud Computing (CC) paradigm has been a good approach for tasks where latency is not critical, but it is not useful when latency matters, so Multi-access Edge Computing (MEC) can be of use. In this work, we propose a distributed Deep Reinforcement Learning (DRL) tool to optimize the binary task offloading decision, this is, the independent decision of where to execute each computing task, depending on many factors. The optimization goal in this work is to maximize the Quality-of-Experience (QoE) when performing tasks, which is defined as a metric related to the battery level of the UE, but subject to satisfying tasks’ latency requirements. This distributed DRL approach, specifically an Actor-Critic (AC) algorithm running on each User Equipment (UE), is evaluated through the simulation of two distinct scenarios and outperforms other analyzed baselines in terms of QoE values and/or energy consumption in dynamic environments, also demonstrating that decisions need to be adapted to the environment’s evolution.
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- 2024
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21. A nursing intervention based on the Zentangle® method: Experiences of patients diagnosed with borderline personality disorder
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Ana Morales-Alonso, Ángela Iglesias-de-la-Iglesia, and Miriam Alonso-Maza
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Art therapy ,Borderline personality disorder ,Mental health ,Nursing care ,Zentangle ,Nursing ,RT1-120 - Abstract
Objective: The application of the Zentangle® Method in relation to relaxation and well-being has not been tested in patients with borderline personality disorder (BPD). This study was to analyze the practising Zentangle® experience in patients with BPD. Methods: With a phenomenological interpretative approach, this qualitative study conducted semi-structured interviews with patients who participated in a 6-session Zentangle® program accomplished monthly over six months in a Personality Disorders Unit. A total of 15 patients were interviewed for this study. Smith, Flowers & Larkin method was applied for evaluation in the data analysis. Results: Based on our findings, three categories were extracted: As you sow, so shall you reap (participants reported improvements in concentration, relaxation, interpersonal relationships, and interaction with their environment as well as positive experiences toward acceptance and change); Many hands make light work (patients admitted feeling better in a group and developed group membership. They described how a group environment influences individual behavior); Drawing your own path (this method provides a medium for self-expression and self-knowledge through drawing, improving well-being through emotional expression, enhancing creativity, and increasing self-confidence). Conclusions: By practicing Zentangle®, patients achieve behavioral responses such as flexibility and adaptability, reaching greater emotional well-being through anxiety management, impulse control, learning to cope with problems, or improving self-esteem or concentration. Mental health nursing plays a critical active role in the comprehensive treatment of BPD, as well as the mobilization and coordination of complementary and diverse interventions.
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- 2024
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22. Autopresentación online auténtica: ¿cómo medirla?, ¿está relacionada con la personalidad, la salud mental y la conducta en línea?
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Guadalupe de la Iglesia and Alejandro Castro Solano
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autopresentación ,online ,rasgos positivos ,personalidad ,integridad ,bienestar ,salud mental ,Psychology ,BF1-990 - Abstract
En este trabajo se analiza la autopresentación online auténtica (AOA): grado en que las personas se presentan de manera online de modo auténtico, sin distorsionar su modo de ser offline. Primero se diseñó una medida psicométrica para su operacionalización, y luego se estudió su asociación con aspectos psicológicos positivos (bienestar y satisfacción con la vida), negativos (síntomas psicológicos y uso problemático de internet) y rasgos de personalidad (normales, patológicos y positivos). Finalmente, se analizó un modelo explicativo en donde la AOA era mediadora entre la personalidad y aspectos psicológicos positivos. Se analizó una muestra de 384 participantes (46.6% hombres, 52.6% mujeres y 0.05% no binarios) con edad promedio de 28 años (DE = 5.92) y una muestra adicional para el análisis factorial confirmatorio de características similares. Se obtuvo buena evidencia de validez (e. g., CFI = .917, SMRS = .059) y confiabilidad (α = .79, ω = .85) para una medida de ocho elementos. La AOA se relaciona positivamente con el bienestar y la satisfacción con la vida, y negativamente con la sintomatología psicológica y el uso problemático de internet. Se encontraron asociaciones positivas con todos los rasgos positivos y con extraversión, agradabilidad y responsabilidad. Se hallaron relaciones negativas con desapego y desinhibición. Los rasgos positivos resultaron ser los más explicativos de la AOA. Se halló que la AOA media la relación entre el rasgo de integridad y la satisfacción con la vida y el bienestar. Se destaca el rol primordial de los rasgos positivos en este tipo de conducta online y con los aspectos positivos asociados a la AOA.
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- 2024
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23. Experimental and numerical analysis of flow through a natural rough fracture subject to normal loading
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Paolo Trinchero, Liangchao Zou, Miquel de La Iglesia, Aitor Iraola, Patrick Bruines, and Guido Deissmann
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Medicine ,Science - Abstract
Abstract Fractured crystalline rocks have been chosen or are under consideration by several countries as host rock formations for deep geological repositories for spent nuclear fuel. In such geological formations, flow and solute transport are mostly controlled by a network of connected natural fractures, each of them being characterised by internal heterogeneity, also denoted as roughness. Fractures are, in turn, subject to variable load caused by various factors, such as the presence of thick ice sheets formed during glaciation periods. Understanding how coupled hydro-mechanical (HM) processes affect flow and transport at the scale of a single natural fracture is crucial for a robust parameterisation of large-scale discrete fracture network models, which are not only used for nuclear waste disposal applications but are also of interest to problems related to geothermics, oil and gas production or groundwater remediation. In this work, we analyse and model an HM experiment carried out in a single natural fracture and use the results of both, the experimental and the modelling work, to get insights into fundamental questions such as the applicability of local cubic law or the effect of normal load on channeling. The initial fracture aperture was obtained from laser scanning of the two fracture surfaces and an equivalent initial aperture was then defined by moving the two fracture surfaces together and comparing the results obtained using a Navier–Stokes based computational fluid dynamics (CFD) model with the experimental flowrate obtained for unloaded conditions. The mechanical effect of the different loading stages was simulated using a high-resolution contact model. The different computed fracture apertures were then used to run groundwater flow simulations using a modified Reynolds equation. The results show that, without correction, local cubic law largely overestimates flowrates. Instead, we show that by explicitly acknowledging the difference between the mechanical aperture and the hydraulic aperture and setting the latter equal to 1/5 of the former, cubic law provides a very reasonable approximation of the experimental flowrates over the entire loading cycle. A positive correlation between fluid flow channeling and normal load is also found.
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- 2024
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24. Machine learning approaches for COVID-19 detection from chest X-ray imaging: A Systematic Review
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Arteaga-Arteaga, Harold Brayan, delaPava, Melissa, Mora-Rubio, Alejandro, Bravo-Ortíz, Mario Alejandro, Alzate-Grisales, Jesus Alejandro, Arias-Garzón, Daniel, López-Murillo, Luis Humberto, Buitrago-Carmona, Felipe, Villa-Pulgarín, Juan Pablo, Mercado-Ruiz, Esteban, Orozco-Arias, Simon, Hassaballah, M., de la Iglesia-Vaya, Maria, Cardona-Morales, Oscar, and Tabares-Soto, Reinel
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
There is a necessity to develop affordable, and reliable diagnostic tools, which allow containing the COVID-19 spreading. Machine Learning (ML) algorithms have been proposed to design support decision-making systems to assess chest X-ray images, which have proven to be useful to detect and evaluate disease progression. Many research articles are published around this subject, which makes it difficult to identify the best approaches for future work. This paper presents a systematic review of ML applied to COVID-19 detection using chest X-ray images, aiming to offer a baseline for researchers in terms of methods, architectures, databases, and current limitations.
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- 2022
25. The 2021 SIIM-FISABIO-RSNA Machine Learning COVID-19 Challenge: Annotation and Standard Exam Classification of COVID-19 Chest Radiographs.
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Lakhani, Paras, Mongan, J, Singhal, C, Zhou, Q, Andriole, K, Auffermann, W, Prasanna, P, Pham, T, Peterson, Michael, Bergquist, P, Cook, T, Ferraciolli, S, Corradi, G, Takahashi, M, Workman, C, Parekh, M, Kamel, S, Galant, J, Mas-Sanchez, A, Benítez, E, Sánchez-Valverde, M, Jaques, L, Panadero, M, Vidal, M, Culiañez-Casas, M, Angulo-Gonzalez, D, Langer, S, de la Iglesia-Vayá, María, and Shih, G
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Artificial Intelligence ,COVID-19 ,Machine Learning ,Pneumonia ,Radiography ,Thorax ,Humans ,COVID-19 ,Artificial Intelligence ,Radiography ,Machine Learning ,Radiologists ,Radiography ,Thoracic - Abstract
We describe the curation, annotation methodology, and characteristics of the dataset used in an artificial intelligence challenge for detection and localization of COVID-19 on chest radiographs. The chest radiographs were annotated by an international group of radiologists into four mutually exclusive categories, including typical, indeterminate, and atypical appearance for COVID-19, or negative for pneumonia, adapted from previously published guidelines, and bounding boxes were placed on airspace opacities. This dataset and respective annotations are available to researchers for academic and noncommercial use.
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- 2023
26. Identification of predictive models including polymorphisms in cytokines genes and clinical variables associated with post-transplant complications after identical HLA-allogeneic stem cell transplantation
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Paula Muñiz, María Martínez-García, Rebeca Bailén, María Chicano, Gillen Oarbeascoa, Juan Carlos Triviño, Ismael de la Iglesia-San Sebastian, Sara Fernández de Córdoba, Javier Anguita, Mi Kwon, José Luis Díez-Martín, Pablo M. Olmos, Carolina Martínez-Laperche, and Ismael Buño
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polymorphisms ,graft-versus-host-disease ,predictive models ,cytokines ,allogeneic transplantation ,Immunologic diseases. Allergy ,RC581-607 - Abstract
BackgroundsAlthough allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potentially curative therapy for hematological malignancies, it can be associated with relevant post-transplant complications. Several reports have shown that polymorphisms in immune system genes are correlated with the development of post-transplant complications. Within this context, this work focuses on identifying novel polymorphisms in cytokine genes and developing predictive models to anticipate the risk of developing graft-versus-host disease (GVHD), transplantation-related mortality (TRM), relapse and overall survival (OS).MethodsOur group developed a 132-cytokine gene panel which was tested in 90 patients who underwent an HLA-identical sibling-donor allo-HSCT. Bayesian logistic regression (BLR) models were used to select the most relevant variables. Based on the cut-off points selected for each model, patients were classified as being at high or low-risk for each of the post-transplant complications (aGVHD II-IV, aGVHD III-IV, cGVHD, mod-sev cGVHD, TRM, relapse and OS).ResultsA total of 737 polymorphisms were selected from the custom panel genes. Of these, 41 polymorphisms were included in the predictive models in 30 cytokine genes were selected (17 interleukins and 13 chemokines). Of these polymorphisms, 5 (12.2%) were located in coding regions, and 36 (87.8%) in non-coding regions. All models had a statistical significance of p
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- 2024
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27. The interplay between climatic niche evolution, polyploidy and reproductive traits explains plant speciation in the Mediterranean Basin: a case study in Centaurium (Gentianaceae)
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Ana Valdés-Florido, Virginia Valcárcel, Enrique Maguilla, Zoila Díaz-Lifante, Cristina Andrés-Camacho, Louis Zeltner, Marina Coca-de-la-Iglesia, Nagore G. Medina, Juan Arroyo, and Marcial Escudero
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centauries ,climatic niche ,chromosome evolution ,Mediterranean climate ,phylogeny ,polyploidy ,Plant culture ,SB1-1110 - Abstract
Speciation and diversification patterns in angiosperms are frequently shaped by niche evolution. Centaurium Hill is a Mediterranean genus with ca. 25 species, of which 60% are polyploids (tetra- and hexaploids), distributed mainly in the Mediterranean Basin and in areas with temperate and arid climates of Asia, Europe, North-Central Africa and North America. The evolutionary history of this genus has been studied using morphological, biogeographical and molecular approaches, but its climatic niche characterization and its relation with genome evolution (chromosome number and ploidy level) has not been addressed yet. Thus, this study aims to identify the role of the evolution of climatic niche, ploidy level, life cycle and floral traits in the diversification of Centaurium. Climatic niche characterization involved estimating present climate preferences using quantitative data and reconstructing ancestral niches to evaluate climatic niche shifts. The evolution of climatic niche towards selective optima determined by ploidy level (three ploidy levels) and different binary traits (polyploidy, floral size, floral display, herkogamy and life cycle) was addressed under the Ornstein-Uhlenbeck model. Chromosome number evolution was inferred using the ChromoSSE model, testing if changes are clado- or anagenetic. Chromosome number evolution and its link with cladogenesis, life cycle and floral traits was modeled on the phylogeny. The reconstruction of the ancestral niches shows that Centaurium originated in a mild climate and diversified to both humid and cold as well as to dry and warmer climates. Niche conservatism was estimated in the climatic niche of the ancestors, while the climatic niche of the current taxa experienced transitions from their ancestors’ niche. Besides, the evolution of climatic niche towards multiple selective optima determined by the studied traits was supported, life cycle optima receiving the highest support. The reconstruction of chromosome number transitions shows that the rate of speciation process resulting from chromosomal changes (chromosomal cladogenesis) is similar to that of non-chromosomal cladogenesis. Additionally, dependent evolution of floral size, floral display and herkogamy with chromosome number variation was supported. In conclusion, polyploidization is a crucial process in the Mediterranean region that assisted speciation and diversification into new areas with different climates, entailing niche shifts and evolution of reproductive strategies.
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- 2024
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28. El proyecto arquitectónico contemporáneo en paisajes arqueológicos de Castilla y León
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Darío Álvarez Álvarez and Miguel Ángel De la Iglesia Santamaría
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proyecto arquitectónico ,paisajes arqueológicos ,Castilla y León ,LAB.PAP ,Architecture ,NA1-9428 ,Urbanization. City and country ,HT361-384 - Abstract
El LAB.PAP Laboratorio de Paisaje Arquitectónico, Patrimonial y Cultural es un Grupo de Investigación Reconocido de la Escuela Técnica Superior de Arquitectura de la Universidad de Valladolid. Está integrado por profesores arquitectos cuyo trabajo es la realización de proyectos de intervención en los paisajes patrimoniales de Castilla y León, con especial dedicación a los paisajes arqueológicos, elaborando para ello una metodología específica y unos mecanismos personales, fruto de la larga experiencia. A lo largo de los últimos años se ha ocupado de proyectos en lugares tan emblemáticos como la ciudad romana de Colonia Clunia Sulpicia en Burgos, la ciudad celtíbero-romana de Tiermes en Soria, el Paisaje Cultural de Las Médulas en León, así como en villas y calzadas romanas. El objetivo de sus proyectos y actuaciones es hacer visible un patrimonio muy rico, pero de una gran fragilidad, para su conservación e investigación y también para hacerlo más comprensible para el turismo cultural de calidad.
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- 2024
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29. Assessment of performance and comparison of three commercial HDV RNA detection assays: implications for diagnosis and treatment monitoring
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Marta Illescas-López, Lucía Chaves-Blanco, Adolfo de Salazar, Melisa Hernández-Febles, Raquel Carracedo, Eduardo Lagarejos, Ana Fuentes, Sara Pereira, Maria Cea, Alberto De La Iglesia, Carolina Freyre, Asunción Iborra, Valle Odero, Aurora García-Barrionuevo, Antonio Aguilera, María José Pena, and Federico García
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hepatitis delta virus ,molecular diagnosis ,RT-PCR ,viral hepatitis ,HDV screening ,Microbiology ,QR1-502 - Abstract
ObjectivesPrecise HDV-RNA detection and quantification are pivotal for diagnosis and monitoring of response to newly approved treatment. We evaluate the performance of three HDV RNA detection and quantification assays.MethodsHepatitis Delta RT-PCR system kit, EurobioPlex HDV assay, and RoboGene HDV RNA Quantification kit 2.0 were used for testing 151 HBsAg-positive samples, 90 HDV-RNA negative and 61 HDV-RNA positive. We also evaluated serial dilutions of the WHO international standard for HDV, PEI 7657/12. All HDV-RNA positive samples were genotyped using a next-generation sequencing strategy.ResultsQualitative results indicated a 100% concordance between tests. Quantitative results correlated well, r2 = 0.703 (Vircell-vs-Eurobio), r2 = 0.833 (Vircell-vs-RoboGene), r2 = 0.835 (Robogene-vs-Eurobio). Bias index was 2.083 (Vircell-vs-Eurobio), -1.283 (Vircell-vs-RoboGene), and -3.36 (Robogene-vs-Eurobio). Using the WHO IS, Vircell overestimated the viral load by 0.98 log IU/mL, Eurobio by 1.46 log IU/mL, and RoboGene underestimated it by 0.98 log IU/mL. Fifty-nine samples were successfully genotyped (Genotype 1, n=52; Genotype 5, n=7; Genotype 6, n=1), with similar results for correlation and bias.ConclusionThis study underscores the necessity of using reliable HDV-RNA detection and quantification assays, as evidenced by the high concordance rates in qualitative detection and the observed variability in quantitative results. These findings highlight the importance of consistent assay use in clinical practice to ensure accurate diagnosis and effective treatment monitoring of HDV infection.
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- 2024
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30. High rate of species misidentification reduces the taxonomic certainty of European biodiversity databases of ivies (Hedera L.)
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Marina Coca-de-la-Iglesia, Angélica Gallego-Narbón, Alejandro Alonso, and Virginia Valcárcel
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Medicine ,Science - Abstract
Abstract The digitization of natural history specimens and the popularization of citizen science are creating an unprecedented availability of large amounts of biodiversity data. These biodiversity inventories can be severely affected by species misidentification, a source of taxonomic uncertainty that is rarely acknowledged in biodiversity data management. For these reasons, taxonomists debate the use of online repositories to address biological questions at the species level. Hedera L. (ivies) provides an excellent case study as it is well represented in both herbaria and online repositories with thousands of records likely to be affected by high taxonomic uncertainty. We analyze the sources and extent of taxonomic errors in the identification of the European ivy species by reviewing herbarium specimens and find a high misidentification rate (18% on average), which varies between species (maximized in H. hibernica: 55%; H. azorica: 48%; H. iberica: 36%) and regions (maximized in the UK: 38% and Spain: 27%). We find a systematic misidentification of all European ivies with H. helix behind the high misidentification rates in herbaria and warn of even higher rates in online records. We compile a spatial database to overcome the large discrepancies we observed in species distributions between online and morphologically reviewed records.
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- 2024
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31. Converging and evolving immuno-genomic routes toward immune escape in breast cancer
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Juan Blanco-Heredia, Carla Anjos Souza, Juan L. Trincado, Maria Gonzalez-Cao, Samuel Gonçalves-Ribeiro, Sara Ruiz Gil, Dmytro Pravdyvets, Samandhy Cedeño, Maurizio Callari, Antonio Marra, Andrea M. Gazzo, Britta Weigelt, Fresia Pareja, Theodore Vougiouklakis, Achim A. Jungbluth, Rafael Rosell, Christian Brander, Francesc Tresserra, Jorge S. Reis-Filho, Daniel Guimarães Tiezzi, Nuria de la Iglesia, Holger Heyn, and Leticia De Mattos-Arruda
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Science - Abstract
Abstract The interactions between tumor and immune cells along the course of breast cancer progression remain largely unknown. Here, we extensively characterize multiple sequential and parallel multiregion tumor and blood specimens of an index patient and a cohort of metastatic triple-negative breast cancers. We demonstrate that a continuous increase in tumor genomic heterogeneity and distinct molecular clocks correlated with resistance to treatment, eventually allowing tumors to escape from immune control. TCR repertoire loses diversity over time, leading to convergent evolution as breast cancer progresses. Although mixed populations of effector memory and cytotoxic single T cells coexist in the peripheral blood, defects in the antigen presentation machinery coupled with subdued T cell recruitment into metastases are observed, indicating a potent immune avoidance microenvironment not compatible with an effective antitumor response in lethal metastatic disease. Our results demonstrate that the immune responses against cancer are not static, but rather follow dynamic processes that match cancer genomic progression, illustrating the complex nature of tumor and immune cell interactions.
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- 2024
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32. Virus-like particle-mediated delivery of structure-selected neoantigens demonstrates immunogenicity and antitumoral activity in mice
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Ana Barajas, Pep Amengual-Rigo, Anna Pons-Grífols, Raquel Ortiz, Oriol Gracia Carmona, Victor Urrea, Nuria de la Iglesia, Juan Blanco-Heredia, Carla Anjos-Souza, Ismael Varela, Benjamin Trinité, Ferran Tarrés-Freixas, Carla Rovirosa, Rosalba Lepore, Miguel Vázquez, Leticia de Mattos-Arruda, Alfonso Valencia, Bonaventura Clotet, Carmen Aguilar-Gurrieri, Victor Guallar, Jorge Carrillo, and Julià Blanco
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Neoantigen ,Cancer vaccine ,Virus-like particle ,Immunotherapy ,T cell response ,Medicine - Abstract
Abstract Background Neoantigens are patient- and tumor-specific peptides that arise from somatic mutations. They stand as promising targets for personalized therapeutic cancer vaccines. The identification process for neoantigens has evolved with the use of next-generation sequencing technologies and bioinformatic tools in tumor genomics. However, in-silico strategies for selecting immunogenic neoantigens still have very low accuracy rates, since they mainly focus on predicting peptide binding to Major Histocompatibility Complex (MHC) molecules, which is key but not the sole determinant for immunogenicity. Moreover, the therapeutic potential of neoantigen-based vaccines may be enhanced using an optimal delivery platform that elicits robust de novo immune responses. Methods We developed a novel neoantigen selection pipeline based on existing software combined with a novel prediction method, the Neoantigen Optimization Algorithm (NOAH), which takes into account structural features of the peptide/MHC-I interaction, as well as the interaction between the peptide/MHC-I complex and the TCR, in its prediction strategy. Moreover, to maximize neoantigens’ therapeutic potential, neoantigen-based vaccines should be manufactured in an optimal delivery platform that elicits robust de novo immune responses and bypasses central and peripheral tolerance. Results We generated a highly immunogenic vaccine platform based on engineered HIV-1 Gag-based Virus-Like Particles (VLPs) expressing a high copy number of each in silico selected neoantigen. We tested different neoantigen-loaded VLPs (neoVLPs) in a B16-F10 melanoma mouse model to evaluate their capability to generate new immunogenic specificities. NeoVLPs were used in in vivo immunogenicity and tumor challenge experiments. Conclusions Our results indicate the relevance of incorporating other immunogenic determinants beyond the binding of neoantigens to MHC-I. Thus, neoVLPs loaded with neoantigens enhancing the interaction with the TCR can promote the generation of de novo antitumor-specific immune responses, resulting in a delay in tumor growth. Vaccination with the neoVLP platform is a robust alternative to current therapeutic vaccine approaches and a promising candidate for future personalized immunotherapy.
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- 2024
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33. The role of microRNAs in understanding sex-based differences in Alzheimer’s disease
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Jaime Llera-Oyola, Héctor Carceller, Zoraida Andreu, Marta R. Hidalgo, Irene Soler-Sáez, Fernando Gordillo, Borja Gómez-Cabañes, Beatriz Roson, Maria de la Iglesia-Vayá, Roberta Mancuso, Franca R. Guerini, Akiko Mizokami, and Francisco García-García
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Sex-based differences ,Alzheimer’s disease ,Biomarkers ,Systematic review ,Meta-analysis ,Transcriptomics ,Medicine ,Physiology ,QP1-981 - Abstract
Abstract Background The incidence of Alzheimer's disease (AD)—the most frequent cause of dementia—is expected to increase as life expectancies rise across the globe. While sex-based differences in AD have previously been described, there remain uncertainties regarding any association between sex and disease-associated molecular mechanisms. Studying sex-specific expression profiles of regulatory factors such as microRNAs (miRNAs) could contribute to more accurate disease diagnosis and treatment. Methods A systematic review identified six studies of microRNA expression in AD patients that incorporated information regarding the biological sex of samples in the Gene Expression Omnibus repository. A differential microRNA expression analysis was performed, considering disease status and patient sex. Subsequently, results were integrated within a meta-analysis methodology, with a functional enrichment of meta-analysis results establishing an association between altered miRNA expression and relevant Gene Ontology terms. Results Meta-analyses of miRNA expression profiles in blood samples revealed the alteration of sixteen miRNAs in female and 22 miRNAs in male AD patients. We discovered nine miRNAs commonly overexpressed in both sexes, suggesting a shared miRNA dysregulation profile. Functional enrichment results based on miRNA profiles revealed sex-based differences in biological processes; most affected processes related to ubiquitination, regulation of different kinase activities, and apoptotic processes in males, but RNA splicing and translation in females. Meta-analyses of miRNA expression profiles in brain samples revealed the alteration of six miRNAs in female and four miRNAs in male AD patients. We observed a single underexpressed miRNA in female and male AD patients (hsa-miR-767-5p); however, the functional enrichment analysis for brain samples did not reveal any specifically affected biological process. Conclusions Sex-specific meta-analyses supported the detection of differentially expressed miRNAs in female and male AD patients, highlighting the relevance of sex-based information in biomedical data. Further studies on miRNA regulation in AD patients should meet the criteria for comparability and standardization of information.
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- 2024
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34. vol2Brain: A new online Pipeline for whole Brain MRI analysis
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Manjon, Jose V., Romero, Jose E., Vivo-Hernando, Roberto, Rubio, Gregorio, Aparici, Fernando, de la Iglesia-Vaya, Mariam, and Coupe, Pierrick
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Quantitative Biology - Quantitative Methods ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
Automatic and reliable quantitative tools for MR brain image analysis are a very valuable resources for both clinical and research environments. In the last years, this field has experienced many advances with successful techniques based on label fusion and more recently deep learning. However, few of them have been specifically designed to provide a dense anatomical labelling at multiscale level and to deal with brain anatomical alterations such as white matter lesions. In this work, we present a fully automatic pipeline (vol2Brain) for whole brain segmentation and analysis which densely labels (N>100) the brain while being robust to the presence of white matter lesions. This new pipeline is an evolution of our previous volBrain pipeline that extends significantly the number of regions that can be analyzed. Our proposed method is based on a fast multiscale multi-atlas label fusion technology with systematic error correction able to provide accurate volumetric information in few minutes. We have deployed our new pipeline within our platform volBrain (www.volbrain.upv.es) which has been already demonstrated to be an efficient and effective manner to share our technology with users worldwide
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- 2022
35. Discharge protocol in acute pancreatitis: an international survey and cohort analysis
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Rita Nagy, Klementina Ocskay, Zoltán Sipos, Andrea Szentesi, Áron Vincze, László Czakó, Ferenc Izbéki, Natalia V. Shirinskaya, Vladimir L. Poluektov, Alexandr N. Zolotov, Yin Zhu, Liang Xia, Wenhua He, Robert Sutton, Peter Szatmary, Rajarshi Mukherjee, Isobel Saffron Burridge, Emma Wauchope, Elsa Francisco, David Aparicio, Bruno Pinto, António Gomes, Vitor Nunes, Vasile Marcel Tantau, Emanuela Denisa Sagau, Alina Ioana Tantau, Andra Iulia Suceveanu, Cristina Tocia, Andrei Dumitru, Elizabeth Pando, Piero Alberti, Arturo Cirera, Xavier Molero, Hong Sik Lee, Min Kyu Jung, Eui Joo Kim, Sanghyub Lee, María Lourdes Ruiz Rebollo, Reyes Busta Nistal, Sandra Izquierdo Santervas, Dusan Lesko, Marek Soltes, Jozef Radonak, Hubert Zatorski, Ewa Małecka-Panas, Adam Fabisiak, M. Susak Yaroslav, V. Maksymenko Mykhailo, A. Tkachenko Olekcandr, Giedrius Barauskas, Vytautas Simanaitis, Povilas Ignatavicius, Mariana Jinga, Vasile-Daniel Balaban, Cristina Patoni, Liang Gong, Kai Song, Yunlong Li, T. Cúrdia Gonçalves, Marta Freitas, Vítor Macedo, Marlies Vornhuelz, Sarah Klauss, Georg Beyer, Aydin Seref Koksal, Mukaddes Tozlu, Ahmet Tarik Eminler, Nuria Torres Monclús, Eva Pijoan Comas, Juan Armando Rodriguez Oballe, Łukasz Nawacki, Stanisław Głuszek, Alberto Rama-Fernández, Marco Galego, Daniel de la Iglesia, Umut Emre Aykut, Deniz Güney Duman, Rahmi Aslan, Adriana Gherbon, Lihui Deng, Wei Huang, Qing Xia, Goran Poropat, Anja Radovan, Luka Vranić, Claudio Ricci, Carlo Ingaldi, Riccardo Casadei, Ionut Negoi, Cezar Ciubotaru, Florin Mihail Iordache, Gabriel Constantinescu, Vasile Sandru, Engin Altintas, Hatice Rizaoglu Balci, Júlio Constantino, Débora Aveiro, Jorge Pereira, Suleyman Gunay, Seda Misirlioglu Sucan, Oleksiy Dronov, Inna Kovalska, Nikhil Bush, Surinder Singh Rana, Serge Chooklin, Serhii Chuklin, Ionut Adrian Saizu, Cristian Gheorghe, Philipp Göltl, Michael Hirth, Radu Bogdan Mateescu, Geanina Papuc, Georgi Angelov Minkov, Emil Tihomirov Enchev, Laura Mastrangelo, Elio Jovine, Weiwei Chen, Quping Zhu, Anita Gąsiorowska, Natalia Fabisiak, Mihailo Bezmarevic, Andrey Litvin, Martina Cattani Mottes, Eun Kwang Choi, Peter Bánovčin, Lenka Nosáková, Mila Dimitrova Kovacheva-Slavova, Ali Kchaou, Ahmed Tlili, Marco V. Marino, Katarzyna Kusnierz, Artautas Mickevicius, Marcus Hollenbach, Pavol Molcan, Orestis Ioannidis, Mark Valerievich Tokarev, Ali Tüzün Ince, Ivan Albertovich Semenenko, Shamil Galeev, Elena Ramírez-Maldonado, Ville Sallinen, Petr Pencik, Judit Bajor, Patricia Sarlós, Roland Hágendorn, Szilárd Gódi, Imre Szabó, József Czimmer, Gabriella Pár, Anita Illés, Nándor Faluhelyi, Péter Kanizsai, Tamás Nagy, Alexandra Mikó, Balázs Németh, József Hamvas, Barnabás Bod, Márta Varga, Imola Török, János Novák, Árpád Patai, János Sümegi, Csaba Góg, Mária Papp, Bálint Erőss, Szilárd Váncsa, Brigitta Teutsch, Katalin Márta, Péter Jenő Hegyi, Tamás Tornai, Balázs Lázár, Tamás Hussein, Dorottya Tarján, Mónika Lipp, Beáta Kovács, Orsolya Urbán, Emese Fürst, Edina Tari, Ibolya Kocsis, Pál Maurovich-Horvát, Balázs Tihanyi, Orsolya Eperjesi, Zita Kormos, Pál Ákos Deák, Andrea Párniczky, and Péter Hegyi
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Medicine ,Science - Abstract
Abstract There are several overlapping clinical practice guidelines in acute pancreatitis (AP), however, none of them contains suggestions on patient discharge. The Hungarian Pancreatic Study Group (HPSG) has recently developed a laboratory data and symptom-based discharge protocol which needs to be validated. (1) A survey was conducted involving all members of the International Association of Pancreatology (IAP) to understand the characteristics of international discharge protocols. (2) We investigated the safety and effectiveness of the HPSG-discharge protocol. According to our international survey, 87.5% (49/56) of the centres had no discharge protocol. Patients discharged based on protocols have a significantly shorter median length of hospitalization (LOH) (7 (5;10) days vs. 8 (5;12) days) p
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- 2023
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36. Genetic Variants in RANK and OPG Could Influence Disease Severity and Bone Remodeling in Patients with Early Arthritis
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Ana Triguero-Martínez, Marisa Pardines, Nuria Montes, Ana María Ortiz, Alba de la Iglesia-Cedeira, Cristina Valero-Martínez, Javier Martín, Isidoro González-Álvaro, Santos Castañeda, and Amalia Lamana
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early arthritis ,single-nucleotide polymorphisms ,bone remodeling ,bone mineral density ,severity ,osteoimmunology ,Science - Abstract
The aim of this study was to identify single-nucleotide polymorphisms (SNPs) in bone remodeling-related genes associated with disease severity and bone mineral density (BMD) in early arthritis (EA) patients. For this purpose, the genotyping of 552 SNPs located in gene regions of semaphorins 4b, 4d, 4f, DKK1, 2 and 3, sclerostin, OPG, RANK and RANKL was performed using Immunochip from Illumina Inc. in 268 patients from the Princesa Early Arthritis Register Longitudinal (PEARL) study. Measurements of BMD and disease activity were chosen as outcome variables to select SNPs of interest. The relationships of SNPs with the BMD of the forearm, lumbar spine and hip (Hologic-4500 QDR) were analyzed by linear regression adjusted for age, sex, body mass index and presence of anti-citrullinated peptide antibodies (ACPAs). The association of each SNP with activity variables was analyzed by linear regression, logistic regression or ordered logistic regression according to the variable, and multivariate models were adjusted for potentially confounding variables, such as age, sex and presence of ACPAs. These analyses showed that four SNPs located in the genes coding for RANK (TNFRSF11A) and OPG (TNFRSF11B) were significantly associated with clinical variables of severity. SNP rs1805034 located in exon 6 of TNFRSF11A, which causes a non-synonymous (A/V) mutation, showed significant association with BMD and therefore may be considered as a possible biomarker of severity in RA patients. SNPs in the OPG gene showed an association with serum OPG levels and predicted disease activity after two years of follow-up.
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- 2024
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37. Electrifying Strategic Management: Leveraging Electric Vehicles for Sustainable Value Creation?
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Sónia Gouveia, Daniel H. de la Iglesia, José Luís Abrantes, Alfonso J. López Rivero, Elisabete Silva, Eduardo Gouveia, and Vasco Santos
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electric vehicle ,strategic management ,value creation ,sustainability ,digital transformation ,artificial intelligence ,Technology - Abstract
Electric vehicles are an emerging topic in organizations and society. Access to economically and environmentally workable sustainable technologies has become a priority in the face of catastrophic climate change and the discussion surrounding it. This study examines the academic literature to shed light on factors, trends, emerging models, and critical perspectives on electric vehicles and their relationship to value creation, strategic management, and sustainability. This research uses a bibliometric analysis method to explore the dynamic interaction between these essential elements of the literature. The source is the Scopus database. The analysis uses VOSviewer software 1.6.20, focusing on the bibliographic coupling of documents, which was presented as a network visualization map. It emphasizes search terms proving the emerging need for innovation strategies in automotive industry organizations, consumers, and public entities to create value within a global sustainability logic. This study highlights the relationship between the electric vehicle industry and the value creation strategy and sustainability in a digital world.
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- 2024
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38. Correction: MetaFun: unveiling sex-based differences in multiple transcriptomic studies through comprehensive functional meta-analysis
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Pablo Malmierca-Merlo, Rubén Sánchez-Garcia, Rubén Grillo-Risco, Irene Pérez-Díez, José F. Català-Senent, María de la Iglesia-Vayá, Marta R. Hidalgo, and Francisco Garcia-Garcia
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Medicine ,Physiology ,QP1-981 - Published
- 2024
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39. Automated Identification of Cylindrical Cells for Enhanced State of Health Assessment in Lithium-Ion Battery Reuse
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Alejandro H. de la Iglesia, Fernando Lobato Alejano, Daniel H. de la Iglesia, Carlos Chinchilla Corbacho, and Alfonso J. López Rivero
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cylindrical cell identification ,state of health (SoH) ,circular economy ,artificial vision ,optical character recognition (OCR) ,Production of electric energy or power. Powerplants. Central stations ,TK1001-1841 ,Industrial electrochemistry ,TP250-261 - Abstract
Lithium-ion batteries are pervasive in contemporary life, providing power for a vast array of devices, including smartphones and electric vehicles. With the projected sale of millions of electric vehicles globally by 2022 and over a million electric vehicles in Europe alone in the first quarter of 2023, the necessity of securing a sustainable supply of lithium-ion batteries has reached a critical point. As the demand for electric vehicles and renewable energy storage (ESS) systems increases, so too does the necessity to address the shortage of lithium batteries and implement effective recycling and recovery practices. A considerable number of electric vehicle batteries will reach the end of their useful life in the near future, resulting in a significant increase in the number of used batteries. It is of paramount importance to accurately identify the manufacturer and model of cylindrical batteries to ascertain their State of Health (SoH) and guarantee their efficient reuse. This study focuses on the automation of the identification of cylindrical cells through optical character recognition (OCR) and the analysis of the external color of the cell and the anode morphology based on computer vision techniques. This is a novel work in the current limited literature, which aims to bridge the gap between industrialized lithium-ion cell recovery processes and an automated SoH calculation. Accurate battery identification optimizes battery reuse, reduces manufacturing costs and mitigates environmental impact. The results of the work are promising, achieving 90% accuracy in the identification of 18,650 cylindrical cells.
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- 2024
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40. Birth-death chains on a spider: spectral analysis and reflecting-absorbing factorization
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de la Iglesia, Manuel D. and Juarez, Claudia
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Mathematics - Probability ,Mathematics - Classical Analysis and ODEs - Abstract
We consider discrete-time birth-death chains on a spider, i.e. a graph consisting of $N$ discrete half lines on the plane that are joined at the origin. This process can be identified with a discrete-time quasi-birth-death process on the state space $\mathbb{N}_0 \times \{1, 2, \dots, N\},$ represented by a block tridiagonal transition probability matrix. We prove that we can analyze this process by using spectral methods and obtain the $n$-step transition probabilities in terms of a weight matrix and the corresponding matrix-valued orthogonal polynomials (the so-called Karlin-McGregor formula). We also study under what conditions we can get a reflecting-absorbing factorization of the birth-death chain on a spider which can be seen as a stochastic UL block factorization of the transition probability matrix of the quasi-birth-death process. With this factorization we can perform a discrete Darboux transformation and get new families of "almost" birth-death chains on a spider. The spectral matrix associated with the Darboux transformation will be a Geronimus transformation of the original spectral matrix. Finally, we apply our results to the random walk on a spider, i.e. with constant transition probabilities., Comment: 18 pages, 3 figures
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- 2021
41. Automatic Semantic Segmentation of the Lumbar Spine: Clinical Applicability in a Multi-parametric and Multi-centre Study on Magnetic Resonance Images
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Saenz-Gamboa, Jhon Jairo, Domenech, Julio, Alonso-Manjarrés, Antonio, Gómez, Jon A., and de la Iglesia-Vayá, Maria
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Electrical Engineering and Systems Science - Image and Video Processing ,Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning ,92B20, 92C50, 68T07, 68T45, 68U10, 92B10 - Abstract
One of the major difficulties in medical image segmentation is the high variability of these images, which is caused by their origin (multi-centre), the acquisition protocols (multi-parametric), as well as the variability of human anatomy, the severity of the illness, the effect of age and gender, among others. The problem addressed in this work is the automatic semantic segmentation of lumbar spine Magnetic Resonance images using convolutional neural networks. The purpose is to assign a class label to each pixel of an image. Classes were defined by radiologists and correspond to different structural elements like vertebrae, intervertebral discs, nerves, blood vessels, and other tissues. The proposed network topologies are variants of the U-Net architecture. Several complementary blocks were used to define the variants: Three types of convolutional blocks, spatial attention models, deep supervision and multilevel feature extractor. This document describes the topologies and analyses the results of the neural network designs that obtained the most accurate segmentations. Several of the proposed designs outperform the standard U-Net used as baseline, especially when used in ensembles where the output of multiple neural networks is combined according to different strategies., Comment: 19 pages, 9 Figures, 8 Tables; Supplementary Material: 6 pages, 8 Tables
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- 2021
42. Discharge protocol in acute pancreatitis: an international survey and cohort analysis
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Nagy, Rita, Ocskay, Klementina, Sipos, Zoltán, Szentesi, Andrea, Vincze, Áron, Czakó, László, Izbéki, Ferenc, Shirinskaya, Natalia V., Poluektov, Vladimir L., Zolotov, Alexandr N., Zhu, Yin, Xia, Liang, He, Wenhua, Sutton, Robert, Szatmary, Peter, Mukherjee, Rajarshi, Burridge, Isobel Saffron, Wauchope, Emma, Francisco, Elsa, Aparicio, David, Pinto, Bruno, Gomes, António, Nunes, Vitor, Tantau, Vasile Marcel, Sagau, Emanuela Denisa, Tantau, Alina Ioana, Suceveanu, Andra Iulia, Tocia, Cristina, Dumitru, Andrei, Pando, Elizabeth, Alberti, Piero, Cirera, Arturo, Molero, Xavier, Lee, Hong Sik, Jung, Min Kyu, Kim, Eui Joo, Lee, Sanghyub, Rebollo, María Lourdes Ruiz, Nistal, Reyes Busta, Santervas, Sandra Izquierdo, Lesko, Dusan, Soltes, Marek, Radonak, Jozef, Zatorski, Hubert, Małecka-Panas, Ewa, Fabisiak, Adam, Yaroslav, M. Susak, Mykhailo, V. Maksymenko, Olekcandr, A. Tkachenko, Barauskas, Giedrius, Simanaitis, Vytautas, Ignatavicius, Povilas, Jinga, Mariana, Balaban, Vasile-Daniel, Patoni, Cristina, Gong, Liang, Song, Kai, Li, Yunlong, Gonçalves, T. Cúrdia, Freitas, Marta, Macedo, Vítor, Vornhuelz, Marlies, Klauss, Sarah, Beyer, Georg, Koksal, Aydin Seref, Tozlu, Mukaddes, Eminler, Ahmet Tarik, Monclús, Nuria Torres, Comas, Eva Pijoan, Oballe, Juan Armando Rodriguez, Nawacki, Łukasz, Głuszek, Stanisław, Rama-Fernández, Alberto, Galego, Marco, de la Iglesia, Daniel, Aykut, Umut Emre, Duman, Deniz Güney, Aslan, Rahmi, Gherbon, Adriana, Deng, Lihui, Huang, Wei, Xia, Qing, Poropat, Goran, Radovan, Anja, Vranić, Luka, Ricci, Claudio, Ingaldi, Carlo, Casadei, Riccardo, Negoi, Ionut, Ciubotaru, Cezar, Iordache, Florin Mihail, Constantinescu, Gabriel, Sandru, Vasile, Altintas, Engin, Balci, Hatice Rizaoglu, Constantino, Júlio, Aveiro, Débora, Pereira, Jorge, Gunay, Suleyman, Misirlioglu Sucan, Seda, Dronov, Oleksiy, Kovalska, Inna, Bush, Nikhil, Rana, Surinder Singh, Chooklin, Serge, Chuklin, Serhii, Saizu, Ionut Adrian, Gheorghe, Cristian, Göltl, Philipp, Hirth, Michael, Mateescu, Radu Bogdan, Papuc, Geanina, Minkov, Georgi Angelov, Enchev, Emil Tihomirov, Mastrangelo, Laura, Jovine, Elio, Chen, Weiwei, Zhu, Quping, Gąsiorowska, Anita, Fabisiak, Natalia, Bezmarevic, Mihailo, Litvin, Andrey, Mottes, Martina Cattani, Choi, Eun Kwang, Bánovčin, Peter, Nosáková, Lenka, Kovacheva-Slavova, Mila Dimitrova, Kchaou, Ali, Tlili, Ahmed, Marino, Marco V., Kusnierz, Katarzyna, Mickevicius, Artautas, Hollenbach, Marcus, Molcan, Pavol, Ioannidis, Orestis, Tokarev, Mark Valerievich, Ince, Ali Tüzün, Semenenko, Ivan Albertovich, Galeev, Shamil, Ramírez-Maldonado, Elena, Sallinen, Ville, Pencik, Petr, Bajor, Judit, Sarlós, Patricia, Hágendorn, Roland, Gódi, Szilárd, Szabó, Imre, Czimmer, József, Pár, Gabriella, Illés, Anita, Faluhelyi, Nándor, Kanizsai, Péter, Nagy, Tamás, Mikó, Alexandra, Németh, Balázs, Hamvas, József, Bod, Barnabás, Varga, Márta, Török, Imola, Novák, János, Patai, Árpád, Sümegi, János, Góg, Csaba, Papp, Mária, Erőss, Bálint, Váncsa, Szilárd, Teutsch, Brigitta, Márta, Katalin, Hegyi, Péter Jenő, Tornai, Tamás, Lázár, Balázs, Hussein, Tamás, Tarján, Dorottya, Lipp, Mónika, Kovács, Beáta, Urbán, Orsolya, Fürst, Emese, Tari, Edina, Kocsis, Ibolya, Maurovich-Horvát, Pál, Tihanyi, Balázs, Eperjesi, Orsolya, Kormos, Zita, Deák, Pál Ákos, Párniczky, Andrea, and Hegyi, Péter
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- 2023
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43. QBD Processes Associated with Jacobi–Koornwinder Bivariate Polynomials and Urn Models
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Fernández, Lidia and de la Iglesia, Manuel D.
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- 2023
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44. Microglia specific deletion of miR-155 in Alzheimer’s disease mouse models reduces amyloid-β pathology but causes hyperexcitability and seizures
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Aloi, Macarena S., Prater, Katherine E., Sánchez, Raymond E. A., Beck, Asad, Pathan, Jasmine L., Davidson, Stephanie, Wilson, Angela, Keene, C. Dirk, de la Iglesia, Horacio, Jayadev, Suman, and Garden, Gwenn A.
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- 2023
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45. Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies
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Guaita-Cespedes, Maria, Grillo-Risco, Rubén, Hidalgo, Marta R., Fernández-Veledo, Sonia, Burks, Deborah Jane, de la Iglesia-Vayá, María, Galán, Amparo, and Garcia-Garcia, Francisco
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- 2023
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46. Characterizing carbapenemase-producing Escherichia coli isolates from Spain: high genetic heterogeneity and wide geographical spread
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Elias Dahdouh, Laro Gómez-Marcos, Javier E. Cañada-García, Eva Ramírez de Arellano, Aida Sánchez-García, Isabel Sánchez-Romero, Luis López-Urrutia, Pedro de la Iglesia, Alejandro Gonzalez-Praetorius, Jared Sotelo, Daniel Valle-Millares, Isabela Alonso-González, Verónica Bautista, Noelia Lara, Silvia García-Cobos, Emilia Cercenado, Belén Aracil, Jesús Oteo-Iglesias, María Pérez-Vázquez, Spanish Eco-Carba Study Group, Verónica Casquero, Olga Valiente, Almudena Alhambra Mosquera, Alia Eworo Ndongo, Susana Hernando Real, Luis Moisés Ruiz-Velasco, José Leiva, Nieves Balado, Adriana Ortega, Mar Olga Pérez Moreno, Ana Bordes, Cristobal del Rosario Quintana, María Eugenia Portillo, Caridad Sainz de Baranda, Gloria Trujillo, Begoña Palop, Carmen Aldea-Mansilla, Juan Cuadros, Yolanda Gil, Soledad Illescas Fernández-Bermejo, Ana Ramos, Salvador Giner, Antonio Casabella Pernas, M. Pilar Ortega Lafont, María Huertas Vaquero, Isabel Antolín, Ma de los Ángeles Pallarés, Beatriz Iglesias, Frederic Gómez-Bertomeu, Ana Isabel López-Calleja, and Pilar Zamarrón
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carbapenemases ,Escherichia coli ,antibiotic resistance ,virulence factor genes ,whole-genome sequencing ,sequence type ,Microbiology ,QR1-502 - Abstract
IntroductionCarbapenemase-Producing Escherichia coli (CP-Eco) isolates, though less prevalent than other CP-Enterobacterales, have the capacity to rapidly disseminate antibiotic resistance genes (ARGs) and cause serious difficult-to-treat infections. The aim of this study is phenotypically and genotypically characterizing CP-Eco isolates collected from Spain to better understand their resistance mechanisms and population structure.MethodsNinety representative isolates received from 2015 to 2020 from 25 provinces and 59 hospitals Spanish hospitals were included. Antibiotic susceptibility was determined according to EUCAST guidelines and whole-genome sequencing was performed. Antibiotic resistance and virulence-associated genes, phylogeny and population structure, and carbapenemase genes-carrying plasmids were analyzed.Results and discussionThe 90 CP-Eco isolates were highly polyclonal, where the most prevalent was ST131, detected in 14 (15.6%) of the isolates. The carbapenemase genes detected were blaOXA-48 (45.6%), blaVIM-1 (23.3%), blaNDM-1 (7.8%), blaKPC-3 (6.7%), and blaNDM-5 (6.7%). Forty (44.4%) were resistant to 6 or more antibiotic groups and the most active antibiotics were colistin (98.9%), plazomicin (92.2%) and cefiderocol (92.2%). Four of the seven cefiderocol-resistant isolates belonged to ST167 and six harbored blaNDM. Five of the plazomicin-resistant isolates harbored rmt. IncL plasmids were the most frequent (45.7%) and eight of these harbored blaVIM-1. blaOXA-48 was found in IncF plasmids in eight isolates. Metallo-β-lactamases were more frequent in isolates with resistance to six or more antibiotic groups, with their genes often present on the same plasmid/integron. ST131 isolates were associated with sat and pap virulence genes. This study highlights the genetic versatility of CP-Eco and its potential to disseminate ARGs and cause community and nosocomial infections.
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- 2024
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47. Validação de escala para mensurar a carga de trabalho das parteiras
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Lorena Gómez García, Maria Dolores Roldan Valcarcel, Ana Myriam Seva Llor, Maria Fuensanta Hellín Gil, Guadalupe Ruiz Merino, Francisco Javier Navarro Guerrero, and Esperanza De La Iglesia Cano
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Tocologia ,Trabalho de parto ,Carga de trabalho ,Terminologia padronizada em enfermagem ,Gestão de recursos humanos ,Nursing ,RT1-120 - Abstract
Resumo Objetivo Validar a elaboração de uma escala para mensurar a carga de trabalho das parteiras com base na Classificação das Intervenções de Enfermagem (NIC) por meio da sua aplicação multicêntrica em diferentes unidades de parto. Métodos Estudo quantitativo, longitudinal, de caráter multicêntrico, realizado em três hospitais universitários gerais da rede pública de saúde. A amostra foi composta por cinquenta parteiras, que examinaram a validade de construto da escala elaborada, com um total de 370 partos. A coleta de dados iniciou-se por meio da escala elaborada ad hoc pela equipe de pesquisa, contabilizando o tempo e o número médio de intervenções NIC, realizadas a cada nascimento. Resultados As parteiras do estudo estão sujeitas a um aumento na sua carga de trabalho quanto ao número e ao tempo médio gasto na realização das NIC em cada parto atendido. Em sua jornada de trabalho (turno de 12 horas), elas destinam 960,61 minutos (16 horas no turno diurno) e 840,29 minutos (14 horas no turno noturno) para executar suas funções na assistência ao parto. Conclusões Os dados indicam a validade da escala elaborada ad hoc, pois esse instrumento reflete a real carga de trabalho vivenciada pelas parteiras do estudo.
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- 2024
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48. Alanine-based spacers promote an efficient antigen processing and presentation in neoantigen polypeptide vaccines
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Aguilar-Gurrieri, Carmen, Barajas, Ana, Rovirosa, Carla, Ortiz, Raquel, Urrea, Victor, de la Iglesia, Nuria, Clotet, Bonaventura, Blanco, Julià, and Carrillo, Jorge
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- 2023
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49. Upper crossed syndrome in secondary school students: A mixed-method study
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Llanos de-la-Iglesia, MSc, Cristina Bravo, PhD, and Francesc Rubí-Carnacea, PhD
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Focus groups ,Forward head posture ,Forward shoulder posture ,Postural balance ,Posture ,Upper crossed syndrome ,Medicine (General) ,R5-920 - Abstract
الملخص: أهداف البحث: كان الهدف هو تحديد مدى انتشار متلازمة التقاطع العلوي والعوامل المرتبطة بها في المراهقين الإسبان. طريقة البحث: استخدمت الدراسة تصميم طريقة مختلطة تفسيرية متسلسلة. تتألف المرحلة الكمية من دراسة مقطعية تم فيها قياس 45 طالبا باستخدام المسح التصويري وتقييمهم باستخدام استبانات ''كيدو-كندل'' و ''فيزا-تيين''. بعد ذلك ، تم إجراء العديد من الاجتماعات لمناقشة النتائج الكمية. النتائج: أظهرت النتائج انتشارا بنسبة 37.8٪ لمتلازمة التقاطع العلوي، وانتشار 48.9٪ لوضع الرأس الأمامي وانتشار وضع الكتف الأمامي بنسبة 80٪. تم أخذ وضع الكتف الأمامي في الاعتبار عندما كانت الزاوية التي يمثلها تقاطع الخط بين نقطة المنتصف لعظم العضد والعملية الشائكة لـ''سي 7'' أقل من 52 درجة. كان وضع الكتف الأمامي أعلى بشكل ملحوظ في الأولاد منه في الفتيات. عند الأولاد، كانت هناك ارتباطات معتدلة ملحوظة بين وضعية الكتف الأمامية ومؤشر كتلة الجسم وعادات النظافة، وبين وضعية الرأس الأمامية وأسوأ مع استخدام التكنولوجيا. أولئك الذين قدموا متلازمة التقاطع العلوي كان لديهم فروق ذات دلالة إحصائية فيما يتعلق بالأداء المدرسي. بعد تحليل النتائج النوعية، تم تحديد 33 رمزا و 5 فئات. الاستنتاجات: يمكن أن ترتبط متلازمة التقاطع العلوي بعوامل مثل مؤشر كتلة الجسم والأداء المدرسي واستخدام التكنولوجيا والنشاط البدني. يتم إعطاء أهمية كبيرة للتمارين البدنية والوضعية الصحية للجلوس والوقوف في بيئة المراهقين. Abstract: Objective: The study objectives were to identify the prevalence of upper crossed syndrome (UCS) and its associated factors in a population of Spanish adolescents, and to explore these associations through focus groups. Methods: The study used a sequential explanatory mixed method design. The quantitative phase consisted of a cross-sectional study in which 45 students underwent photogrammetry measurements and evaluations with the Kiddo-KINDL and VISA-TEEN questionnaires. Subsequently, several focus groups were conducted to discuss the quantitative results. Results: The results indicated a 37.8% prevalence of UCS, a 48.9% prevalence of forward head posture (FHP) and an 80% prevalence of forward shoulder posture (FSP). A positive FSP was indicated by an angle represented by the intersection of the line between the midpoint of the humerus and the spinous process of C7 of
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- 2023
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50. Empowering tomorrow's leaders: the impact of the 15th Network of Young Researchers in Andrology (NYRA) meeting on male reproductive health and interdisciplinary collaboration
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Daniel Marcu, Dorte L. Egeberg, Guillaume Richer, Brendan Houston, Emily Delgouffe, Gülizar Saritas, Omar Ammar, Lydia Wehrli, Cyril Djari, and Alberto de la Iglesia
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european academy of andrology ,network for young researchers in andrology ,in vitro spermatogenesis ,male infertility ,mammalian reproduction ,sperm physiology ,Science ,Biology (General) ,QH301-705.5 - Published
- 2024
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